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SHELX C/D/E: Difference between revisions
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update SHELXE documentation
(→Phasing and density modification: update shelxe description) |
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shelxe xx yy -m20 -s0.45 -h8 -b | shelxe xx yy -m20 -s0.45 -h8 -b | ||
would do 20 cycles density modification with a solvent content of 0.45, phasing from the first 8 heavy atoms in the yy.res file from SHELXD assuming that they are also present in the native structure (-h8), and then use the modified density to generate improved heavy atoms (-b). The switch -i may be added to invert the substructure (and if necessary the space group), this writes xx_i.phs instead of xx.phs etc., and so may be run in parallel | would do 20 cycles density modification with a solvent content of 0.45, phasing from the first 8 heavy atoms in the yy.res file from SHELXD assuming that they are also present in the native structure (-h8), and then use the modified density to generate improved heavy atoms (-b). The switch -i may be added to invert the substructure (and if necessary the space group), this writes xx_i.phs instead of xx.phs etc., and so may be run in parallel. <br> | ||
A big difference in the contrast between the two heavy-atom enantiomorphs usually indicates a good SHELXE solution. However in the case of SIR, both have the same contrast but one gives the inverted protein structure. The contrast is also the same for both if the heavy-atom substructure is centrosymmetric. In the case of SAD both heavy atom enantiomers then give the correct structure, for SIR the result is an uninterpretable double image. <br> | A big difference in the contrast between the two heavy-atom enantiomorphs usually indicates a good SHELXE solution. However in the case of SIR, both have the same contrast but one gives the inverted protein structure. The contrast is also the same for both if the heavy-atom substructure is centrosymmetric. In the case of SAD both heavy atom enantiomers then give the correct structure, for SIR the result is an uninterpretable double image. <br> | ||
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The new switch -e may be used to extrapolate the data to the specified resolution (the '''''free lunch algorithm'''''), based closely on work by the Bari group (Caliandro ''et al''., ''Acta Crystallogr''. (2005) '''D61''', 556-565) and independently implemented in the program [[Acorn]] (Yao ''et al''., (2005) ''Acta Crystallogr''. '''D61''', 1465-1475): -e1.0 can produce spectacular results when applied to data collected to 1.6 to 2.0 Å, but since a large number of cycles is required (-m400) and the 'contrast' and 'connectivity' become unreliable (the pseudo-free CC is the only reliable map quality indicator when the FLA is used), it may be best to establish the substructure enantiomorph and solvent content without -e first. The default setting when -e is not specified is to fill in missing low and medium resolution data but not to extrapolate to higher resolution than actually measured (to switch off this filling in, use -e999). The resolution requirements for the FLA still need to be explored, but so far there have been no reports of it causing a deterioration in map quality, and in a few cases the mean phase error was reduced by as much as 30º relative to density modification without it.<br> | The new switch -e may be used to extrapolate the data to the specified resolution (the '''''free lunch algorithm'''''), based closely on work by the Bari group (Caliandro ''et al''., ''Acta Crystallogr''. (2005) '''D61''', 556-565) and independently implemented in the program [[Acorn]] (Yao ''et al''., (2005) ''Acta Crystallogr''. '''D61''', 1465-1475): -e1.0 can produce spectacular results when applied to data collected to 1.6 to 2.0 Å, but since a large number of cycles is required (-m400) and the 'contrast' and 'connectivity' become unreliable (the pseudo-free CC is the only reliable map quality indicator when the FLA is used), it may be best to establish the substructure enantiomorph and solvent content without -e first. The default setting when -e is not specified is to fill in missing low and medium resolution data but not to extrapolate to higher resolution than actually measured (to switch off this filling in, use -e999). The resolution requirements for the FLA still need to be explored, but so far there have been no reports of it causing a deterioration in map quality, and in a few cases the mean phase error was reduced by as much as 30º relative to density modification without it.<br> | ||
The -a option sets the number of global autotracing cycles; -a on its own is equivalent to -a3. The current values of all parameters are output at the start of the shelxe output, the default values will rarely need changing | |||
== RIP with SHELXC/D/E == | == RIP with SHELXC/D/E == | ||